Literature DB >> 31921362

Correction to: Nested plant LTR retrotransposons target specific regions of other elements, while all LTR retrotransposons often target palindromes and nucleosome-occupied regions: in silico study.

Pavel Jedlicka1, Matej Lexa2, Ivan Vanat2, Roman Hobza1, Eduard Kejnovsky1.   

Abstract

[This corrects the article DOI: 10.1186/s13100-019-0186-z.].
© The Author(s). 2020.

Entities:  

Year:  2020        PMID: 31921362      PMCID: PMC6947867          DOI: 10.1186/s13100-019-0199-7

Source DB:  PubMed          Journal:  Mob DNA


Correction to: Mobile DNA https://doi.org/10.1186/s13100-019-0186-z Following publication of the original article [1], the authors spotted an error in Table 2.
Table 2

Palindromes within sequences flanking the insertion site. We used the paldpl program to detect approximate palindromes of at least 3 bp with no more than 30% mismatches or indels. This analysis was done in native flanking sequences identified in plant genomes and their randomized (permutated) counterparts, to control for base content effects. We carried out a paired t-test for difference in calculated stem lengths of the native and randomized palindromes. Significant values after Benjamini-Hochberg correction for multiple family testing are marked with an asterisk and printed in bold (* for p < 0.1, ** for p < 0.01 and *** for p < 0.001). Three families with increased mean palindrome stem length after randomization are marked with a tilde

GroupCountPalindrome lengthPaired t-test p-value
native random
ALL14,8135.55.40.000004***
nested 830 5.2 5.3 0.50~
non-nested 13,983 5.5 5.4 0.000001***
Ale13145.55.50.93
Alesia215.85.70.75
Angela915.35.30.93
Athila10885.55.30.008**
Bianca 443 6.0 6.1 0.97~
Bryco 29 5.8 5.9 0.95~
CRM4825.35.20.53
Galadriel495.45.10.40
Ikeros3485.55.30.10
Ivana10185.55.30.008**
Ogre15205.55.40.64
Phygy2855.35.30.94
Reina8525.45.40.67
Retand20785.45.30.37
Sire12255.45.20.001**
Tcn119475.55.40.001**
TAR4775.55.40.14
Tekay10295.45.40.61
Tork 517 5.6 5.8 0.05*~
t-test pvalue in penultimate row = “0.61” should not be bold the asterisks with significance levels should be as follows: “(* for p < 0.1, ** for p < 0.01 and *** for p < 0.001)” The original article has been corrected. The correct presentation of Table 2 is shown below. Palindromes within sequences flanking the insertion site. We used the paldpl program to detect approximate palindromes of at least 3 bp with no more than 30% mismatches or indels. This analysis was done in native flanking sequences identified in plant genomes and their randomized (permutated) counterparts, to control for base content effects. We carried out a paired t-test for difference in calculated stem lengths of the native and randomized palindromes. Significant values after Benjamini-Hochberg correction for multiple family testing are marked with an asterisk and printed in bold (* for p < 0.1, ** for p < 0.01 and *** for p < 0.001). Three families with increased mean palindrome stem length after randomization are marked with a tilde
  1 in total

1.  Nested plant LTR retrotransposons target specific regions of other elements, while all LTR retrotransposons often target palindromes and nucleosome-occupied regions: in silico study.

Authors:  Pavel Jedlicka; Matej Lexa; Ivan Vanat; Roman Hobza; Eduard Kejnovsky
Journal:  Mob DNA       Date:  2019-12-14
  1 in total

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